Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells
Abstract
1. Introduction
2. Materials and Methods
2.1. Cell Culture and Transfection
2.2. Intact Cell NMR Spectroscopy
2.3. Metabolite Extraction
2.4. Aqueous Phase NMR Spectroscopy
2.5. Aqueous Phase Liquid Chromatography–Mass Spectrometry
2.6. Organic-Phase High-Performance Thin-Layer Chromatography
2.7. RNA Extraction and Quantitative RT-PCR
2.8. Univariate Statistics
2.9. OPLS Data Processing of NMR Spectra
2.10. O2PLS of Joint Metabolites/Transcripts
2.11. Pathway Analysis
3. Results
3.1. SUM1315-BRCA1 Intact Cells Exhibit Reduction in Intracellular Fatty Acid Levels
3.2. SUM1315-BRCA1 Water-Soluble Extracts Exhibit Numerous Metabolite Alterations
3.3. Joint Metabolite/Transcript Analysis Using O2PLS Identifies Most Important Metabolites and Genes of Metabolic Reprogramming
3.4. Joint Metabolite/Transcript Analysis Using ORA Identifies Most Important Pathways of Metabolic Reprogramming
3.5. Combining Results of Joint Data Processing
- (1)
- A first metabolism superset was centered around bioenergetic metabolism and contained 7 pathways (‘Central carbon metabolism in cancer’, ‘Citrate cycle (TCA cycle)’, ‘Pyruvate metabolism’, ‘HIF-1 signaling pathway’, ’Pentose phosphate pathway’, ‘Glycolysis or Gluconeogenesis’, and ‘Butanoate metabolism’), 7 downregulated genes (SLC2A1, HK1, HK2, PFKFB3, LDHA, IDH2, and TKT), 8 increased metabolites (Ala, Asp, Leu, Phe, Pro, Tyr, and ATP) and 3 decreased metabolites (For, Acn, and BHB).
- (2)
- A second metabolism superset was centered around glycerophospholipid metabolism and contained 3 pathways (‘Glycerophospholipid metabolism’, ‘Choline metabolism in cancer’, and ‘Inositol phosphate metabolism’), 2 upregulated genes (PTDSS1 and PCYT1A), 2 downregulated genes (CDS1 and CHKA), 1 increased metabolite (MyI), and 2 decreased metabolites (Sci and FFA).
- (3)
- A third metabolism superset was centered around glutathione metabolism and contained 3 pathways (‘Glutathione metabolism’, ‘Cysteine and methionine metabolism’, and ‘Taurine and hypotaurine metabolism’), 5 downregulated genes (GOT2, LDHA, IDH2, ODC1, and GPX1), 9 increased metabolites (GSH, GSx, CyG, Spmd, Asp, MTA, SAH, Ala, and Tau) and 1 decreased metabolite (Ace).
- (4)
- A fourth metabolism superset was centered around nucleic acid metabolism and contained 4 pathways (‘One-carbon pool by folate’, ‘Purine metabolism’, ‘Pantothenate and CoA biosynthesis’ and ‘Pyrimidine metabolism’), 2 downregulated genes (SHMT1 and CTPS2), 10 increased metabolites (Asp, Ade, HpX, Ins, Ads, Ura, Urd, ATP, Bet, and SAH) and 1 decreased metabolite (ADP).
- (5)
- A fifth metabolism superset was centered around Arg metabolism and contained 5 pathways (‘Arginine and proline metabolism’, ‘Alanine, aspartate, and glutamate metabolism’, ‘Glycine, serine, and threonine metabolism’, Arginine biosynthesis’, and ‘Glyoxylate and dicarboxylate metabolism’), 4 downregulated genes (ARG2, ODC1, GOT2, and SHMT1), 7 increased metabolites (Pro, Spmd, Cre, Bet, Trp, Asp, and Ala), and 2 decreased metabolites (NAA and For).
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
BRCA1/BRCA1 | Breast cancer susceptibility gene 1 (gene/protein) |
FA | Fatty acid |
ACC1 | Acetyl-CoA carboxylase 1 |
ROS | Reactive oxygen species |
HIF-1 | Hypoxia-inducible-factor 1 |
GOT2 | Glutamic-oxaloacetic transaminase 2 |
NNMT | Nicotinamide N-methyltransferase |
Ade | Adenine |
PtS | Phosphatidylserine |
PtC | Phosphatidylcholine |
GSH/GSSG | Reduced/oxidized glutathione |
Arg | Arginine |
TNBC | Triple-negative breast cancer |
Cre | Creatine |
OPLS | Orthogonal partial least squares |
CV-ANOVA | Cross-validated ANOVA |
O2PLS | Two-way orthogonal partial least squares |
ORA | Overrepresentation analysis |
GSx | Total glutathione |
tCr | Total creatine |
MyI | Myoinositol |
Tau | Taurine |
Glu | Glutamic acid |
BHB | 3-Hydroxybutyric acid |
NAA | N-acetyl-L-aspartic acid |
PC | Phosphorylcholine |
ScI | Scylloinositol |
TCA | Tricarboxylic acid cycle |
ACoA | Acetyl-CoA |
AKG | Alphaketoglutarate |
NADH | Reduced nicotinamide adenine dinucleotide |
NADPH | Reduced nicotinamide adenine dinucleotide phosphate |
AMPK | AMP-activated protein kinase |
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Lucaora, T.; Morvan, D. Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells. Metabolites 2025, 15, 534. https://doi.org/10.3390/metabo15080534
Lucaora T, Morvan D. Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells. Metabolites. 2025; 15(8):534. https://doi.org/10.3390/metabo15080534
Chicago/Turabian StyleLucaora, Thomas, and Daniel Morvan. 2025. "Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells" Metabolites 15, no. 8: 534. https://doi.org/10.3390/metabo15080534
APA StyleLucaora, T., & Morvan, D. (2025). Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells. Metabolites, 15(8), 534. https://doi.org/10.3390/metabo15080534